Nucleotide sequences coding for the pknD gene

ABSTRACT

An isolated polynucleotide which contains a polynucleotide sequence selected from the group comprising:
         (a) a polynucleotide which is at least 70% identical to a polynucleotide coding for a polypeptide containing the amino acid sequence of SEQ ID No. 2,   (b) a polynucleotide coding for a polypeptide containing an amino acid sequence which is at least 70% identical to the amino acid sequence of SEQ ID No. 2,   (c) a polynucleotide which is complementary to the polynucleotides of (a) or (b), and   (d) a polynucleotide containing at least 15 consecutive nucleotides of the polynucleotide sequence of (a), (b), or (c),   and a fermentation process for the preparation of L-amino acids using corynebacteria in which at least the pknD gene is amplified, and to the use, as hybridization probes, of polynucleotides containing the sequences according to the invention.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application claims benefit to U.S. Provisional Application Ser. No. 60/297,266, filed Jun. 12, 2001 and identified herein by reference.

BACKGROUND OF THE INVENTION

1. Field of the Invention

The present invention provides nucleotide sequences from corynebacteria coding for the pknD gene and a fermentation process for the preparation of amino acids using bacteria in which the endogenous pknD gene is amplified.

2. Description of the Background

L-Amino acids, especially L-lysine, are used in human medicine, in the pharmaceutical industry, in the food industry, and, in particular, in animal nutrition. It is known that amino acids are prepared by the fermentation of strains of corynebacteria, especially Corynebacterium glutamicum. Because of their great importance, attempts are constantly being made to improve such preparative processes. Improvements to these processes may relate to measures involving the fermentation technology, e.g. stirring and oxygen supply, or the composition of the nutrient media, e.g. the sugar concentration during fermentation, or the work-up to the product form, e.g. by ion exchange chromatography, or the intrinsic productivity characteristics of the microorganism itself.

The productivity characteristics of these microorganisms are improved by using methods of mutagenesis, selection and mutant choice to give strains which are resistant to antimetabolites or auxotrophic for metabolites important in regulation, and produce amino acids.

Methods of recombinant DNA technology have also been used for some years to improve L-amino acid-producing strains of Corynebacterium by amplifying individual amino acid biosynthesis genes and studying the effect on amino acid production. However, there remains a need for improved methods of producing L-amino acids.

SUMMARY OF THE INVENTION

It is an object of the present invention to provide novel measures for improving the preparation of amino acids by fermentation.

It is another object of the present invention to provide nucleic acid sequences which are useful for the production of amino acids.

Accordingly, the present invention provides an isolated polynucleotide from corynebacteria which contains a polynucleotide sequence coding for the pknD gene and is selected from the following group:

(a) a polynucleotide which is at least 70% identical to a polynucleotide coding for a polypeptide containing the amino acid sequence of SEQ ID No. 2,

(b) a polynucleotide coding for a polypeptide containing an amino acid sequence which is at least 70% identical to the amino acid sequence of SEQ ID No. 2,

(c) a polynucleotide which is complementary to the polynucleotides of (a) or (b), and

(d) a polynucleotide containing at least 15 consecutive nucleotides of the polynucleotide sequence of (a), (b) or (c),

where the polypeptide preferably has the activity of protein kinase D.

The present invention also provides the above-mentioned polynucleotide, which is preferably a replicable DNA containing:

(i) the nucleotide sequence shown in SEQ ID No. 1, or

(ii) at least one sequence corresponding to sequence (i) within the degeneracy of the genetic code, or

(iii) at least one sequence which hybridizes with the sequence complementary to sequence (i) or (ii), and optionally

(iv) neutral sense mutations in (i).

The present invention additionally provides:

a replicable polynucleotide, especially DNA, containing the nucleotide sequence as shown in SEQ ID No. 1,

a polynucleotide coding for a polypeptide containing the amino acid sequence as shown in SEQ ID No. 2,

a vector containing the polynucleotide according to the invention, especially a shuttle vector or plasmid vector, and

corynebacteria which contain the vector or in which the endogenous pknD gene is amplified.

The present invention additionally provides a fermentation process for the preparation of an L-amino acid, comprising:

(a) fermenting in a medium corynebacteria producing the L-amino acid, wherein at least the endogenous pknD gene or nucleotide sequences coding therefor are amplified in the corynebacteria,

(b) enriching the L-amino acid in the medium or in the cells of the corynebacteria, and

(c) isolating the L-amino acid.

The present invention also provides polynucleotides consisting substantially of a polynucleotide sequence which are obtainable by screening, by means of hybridization, of an appropriate gene library of a Corynebacterium, containing the complete gene or parts thereof, with a probe containing the sequence of the polynucleotide of the invention according to SEQ ID No. 1 or a fragment thereof, and by isolation of the polynucleotide sequence.

BRIEF DESCRIPTION OF THE FIGURE

A more complete appreciation of the invention and many of the attendant advantages thereof will be readily obtained as the same becomes better understood by reference to the following FIGURE in conjunction with the detailed description below.

FIG. 1: Map of the plasmid pK18mobsacB_pknD_XL.

The abbreviations and designations used have the following meaning. The length data are to be understood as approximate values.

-   sacB: sacB gene -   oriV: Replication origin V -   KmR: Kanamycin resistance -   XbaI: Cleavage site of the restriction enzyme XbaI -   pknD′: Incomplete fragment of the pknD gene from DM1547

DETAILED DESCRIPTION OF THE INVENTION

When L-amino acids or amino acids are mentioned hereafter, this is understood to refer to one or more amino acids, including their salts, selected from the group comprising L-asparagine, L-threonine, L-serine, L-glutamate, L-glycine, L-alanine, L-cysteine, L-valine, L-methionine, L-isoleucine, L-leucine, L-tyrosine, L-phenylalanine, L-histidine, L-lysine, L-tryptophan and L-arginine. L-Lysine is particularly preferred.

When L-lysine or lysine is mentioned hereafter, this is understood to refer to not only the bases but also the salts, e.g. lysine monohydrochloride or lysine sulfate.

As hybridization probes for RNA, cDNA and DNA, polynucleotides containing the sequences according to the invention are suitable for isolating the full length of nucleic acids, or polynucleotides or genes, coding for protein kinase D, or for isolating nucleic acids, or polynucleotides or genes, whose sequence exhibits a high degree of similarity to the sequence of the pknD gene. They are also suitable for incorporation into so-called arrays, micro-arrays or DNA chips for detecting and determining the corresponding polynucleotides. Polynucleotides containing the sequences according to the invention are further suitable as primers for the preparation, by the polymerase chain reaction (PCR), of DNA of genes coding for protein kinase D.

Such oligonucleotides serving as probes or primers contain at least 25, 26, 27, 28, 29 or 30, preferably at least 20, 21, 22, 23 or 24 and very particularly preferably at least 15, 16, 17, 18 or 19 consecutive nucleotides. Oligonucleotides with a length of at least 31, 32, 33, 34, 35, 36, 37, 38, 39 or 40 or at least 41, 42, 43, 44, 45, 46, 47, 48, 49 or 50 nucleotides are also suitable. Oligonucleotides with a length of at least 100, 150, 200, 250 or 300 nucleotides may also be suitable.

As used herein, the term “isolated” refers to a material, e.g., a nucleic acid, separated from its natural environment.

“Polynucleotide” refers in general to polyribonucleotides and polydeoxyribonucleotides, it being possible for the RNAs or DNAs in question to be unmodified or modified.

The polynucleotides according to the invention include a polynucleotide according to SEQ ID No. 1 or a fragment prepared therefrom, as well as polynucleotides which are in particular at least 70% to 80%, preferably at least 81% to 85%, particularly preferably at least 86% to 90% and very particularly preferably at least 91%, 93%, 95%, 97% or 99% identical to the polynucleotide according to SEQ ID No. 1 or a fragment prepared therefrom. “Polypeptides” are understood as meaning peptides or proteins containing two or more amino acids bonded via peptide links.

The polypeptides according to the invention include a polypeptide according to SEQ ID No. 2, especially those with the biological activity of protein kinase D and also those which are at least 70% to 80%, preferably at least 81% to 85%, particularly preferably at least 86% to 90% and very particularly preferably at least 91%, 93%, 95%, 97% or 99% identical to the polypeptide according to SEQ ID No. 2, and have the activity of protein kinase D.

The invention further relates to a fermentation process for the preparation of amino acids selected from the group comprising L-asparagine, L-threonine, L-serine, L-glutamate, L-glycine, L-alanine, L-cysteine, L-valine, L-methionine, L-isoleucine, L-leucine, L-tyrosine, L-phenylalanine, L-histidine, L-lysine, L-tryptophan and L-arginine, using corynebacteria which, in particular, already produce amino acids and in which the nucleotide sequences coding for the pknD gene are amplified and, in particular, overexpressed.

In this context the term “amplification” describes the increase in the intracellular activity, in a microorganism, of one or more enzymes which are coded for by the appropriate DNA, for example by increasing the copy number of the gene(s) or allele(s), using a strong promoter or using a gene or allele coding for an appropriate enzyme with a high activity, and optionally combining these measures.

By amplification measures, in particular over-expression, the activity or concentration of the corresponding protein is in general increased by at least 10%, 25%, 50%, 75%, 100%, 150%, 200%, 300%, 400% or 500%, up to a maximum of 1000% or 2000%, based on that of the wild-type protein or the activity or concentration of the protein in the starting microorganism.

The microorganisms provided by the present invention can produce L-amino acids from glucose, sucrose, lactose, fructose, maltose, molasses, starch or cellulose or from glycerol and ethanol. The microorganisms can be representatives of corynebacteria, especially of the genus Corynebacterium. The species Corynebacterium glutamicum may be mentioned in particular in the genus Corynebacterium, which is known to those skilled in the art for its ability to produce L-amino acids.

The following known wild-type strains:

-   -   Corynebacterium glutamicum ATCC13032     -   Corynebacterium acetoglutamicum ATCC15806     -   Corynebacterium acetoacidophilum ATCC13870     -   Corynebacterium thermoaminogenes FERM BP-1539     -   Corynebacterium melassecola ATCC17965     -   Brevibacterium flavum ATCC14067     -   Brevibacterium lactofermentum ATCC13869, and     -   Brevibacterium divaricatum ATCC14020         and L-amino acid-producing mutants or strains prepared         therefrom, are particularly suitable strains of the genus         Corynebacterium, especially of the species Corynebacterium         glutamicum (C. glutamicum).

The novel pknD gene of C. glutamicum coding for the enzyme protein kinase D (EC 2.7.1.37) has been isolated using the procedures described herein.

The first step in isolating the pknD gene or other genes of C. glutamicum is to construct a gene library of this microorganism in Escherichia coli (E. coli). The construction of gene libraries is documented in generally well-known textbooks and manuals. Examples which may be mentioned are the textbook by Winnacker entitled From Genes to Clones, Introduction to Gene Technology (Verlag Chemie, Weinheim, Germany, 1990) or the manual by Sambrook et al. entitled Molecular Cloning, A Laboratory Manual (Cold Spring Harbor Laboratory Press, 1989). A very well-known gene library is that of the E. coli K-12 strain W3110, which was constructed by Kohara et al. (Cell 50, 495-508 (1987)) in λ vectors. Bathe et al. (Molecular and General Genetics 252, 255-265, 1996) describe a gene library of C. glutamicum ATCC13032, which was constructed using cosmid vector SuperCos I (Wahl et al., 1987, Proceedings of the National Academy of Sciences USA 84, 2160-2164) in the E. coli K-12 strain NM554 (Raleigh et al., 1988, Nucleic Acids Research 16, 1563-1575). Börmann et al. (Molecular Microbiology 6(3), 317-326 (1992)) in turn describe a gene library of C. glutamicum ATCC 13032 using cosmid pHC79 (Hohn and Collins, Gene 11, 291-298 (1980)).

A gene library of C. glutamicum in E. coli can also be constructed using plasmids like pBR322 (Bolivar, Life Sciences 25, 807-818 (1979)) or pUC9 (Vieira et al., 1982, Gene 19, 259-268). Restriction- and recombination-defective E. coli strains are particularly suitable as hosts, an example being the strain DH5αmcr, which has been described by Grant et al. (Proceedings of the National Academy of Sciences USA 87 (1990) 4645-4649). The long DNA fragments cloned with the aid of cosmids can then in turn be subcloned into common vectors suitable for sequencing, and subsequently sequenced, e.g. as described by Sanger et al. (Proceedings of the National Academy of Sciences of the United States of America 74, 5463-5467, 1977).

The DNA sequences obtained can then be examined with known algorithms or sequence analysis programs, e.g. that of Staden (Nucleic Acids Research 14, 217-232 (1986)), that of Marck (Nucleic Acids Research 16, 1829-1836 (1988)) or the GCG program of Butler (Methods of Biochemical Analysis 39, 74-97 (1998)).

The novel DNA sequence of C. glutamicum coding for the pknD gene was found and, as SEQ ID No. 1, forms part of the present invention. Furthermore, the amino acid sequence of the corresponding protein was derived from the DNA sequence by the methods described above. The resulting amino acid sequence of the pknD gene product is shown in SEQ ID No. 2.

Coding DNA sequences which result from SEQ ID No. 1 due to the degeneracy of the genetic code are also within the scope of the present invention. Likewise, DNA sequences which hybridize with SEQ ID No. 1 or portions of SEQ ID No. 1 are also within the scope of the present invention. Furthermore, conservative amino acid exchanges, e.g. the exchange of glycine for alanine or of aspartic acid for glutamic acid in proteins, are known to those skilled in the art as “sense mutations”, which do not cause a fundamental change in the activity of the protein, i.e. they are neutral. It is also known that changes at the N- and/or C-terminus of a protein do not substantially impair its function or may even stabilize it. Those skilled in the art can find information on this subject in Ben-Bassat et al. (Journal of Bacteriology 169, 751-757 (1987)), O'Regan et al. (Gene 77, 237-251 (1989)), Sahin-Toth et al. (Protein Sciences 3, 240-247 (1994)) and Hochuli et al. (Bio/Technology 6, 1321-1325 (1988)), inter alia, and in well-known textbooks on genetics and molecular biology. Amino acid sequences which correspondingly result from SEQ ID No. 2 are also within the scope of the present invention.

Likewise, DNA sequences which hybridize with SEQ ID No. 1 or portions of SEQ ID No. 1 are also within the scope of the present invention. Finally, DNA sequences which are prepared by the polymerase chain reaction (PCR) using primers resulting from SEQ ID No. 1 are additonally within the scope of the present invention. Such oligonucleotides typically have a length of at least 15 nucleotides.

Those skilled in the art can find instructions on the identification of DNA sequences by means of hybridization in inter alia the manual entitled “The DIG System User's Guide for Filter Hybridization” from Boehringer Mannheim GmbH (Mannheim, Germany, 1993) and in Liebl et al. (International Journal of Systematic Bacteriology (1991) 41, 255-260), inter alia. Hybridization takes place under stringent conditions; in other words, only hybrids for which the probe and the target sequence, i.e. the polynucleotides treated with the probe, are at least 70% identical are formed. It is known that the stringency of hybridization, including the washing steps, is influenced or determined by varying the buffer composition, the temperature and the salt concentration. The hybridization reaction is preferably carried out under relatively low stringency compared with the washing steps (Hybaid Hybridisation Guide, Hybaid Limited, Teddington, UK, 1996).

The hybridization reaction can be carried out for example using a 5×SSC buffer at a temperature of approx. 50° C.-68° C., it also being possible for probes to hybridize with polynucleotides which are less than 70% identical to the sequence of the probe. Such hybrids are less stable and are removed by washing under stringent conditions. This can be achieved for example by lowering the salt concentration to 2×SSC and subsequently to 0.5×SSC if necessary (The DIG System User's Guide for Filter Hybridization, Boehringer Mannheim, Mannheim, Germany, 1995), the temperature being adjusted to approx. 50° C.-68° C. It is possible to lower the salt concentration to 0.1×SSC if necessary. By raising the hybridization temperature in approx. 1-2° C. steps from 50° C. to 68° C., it is possible to isolate polynucleotide fragments which are e.g. at least 70%, at least 80% or at least 90% to 95% identical to the sequence of the probe used. Further instructions on hybridization are commercially available in the form of kits (e.g. DIG Easy Hyb from Roche Diagnostics GmbH, Mannheim, Germany, Catalog No. 1603558).

Those skilled in the art can find instructions on the amplification of DNA sequences with the aid of the polymerase chain reaction (PCR) in the manual by Gait entitled Oligonucleotide Synthesis: A Practical Approach (IRL Press, Oxford, UK, 1984) and in Newton and Graham: PCR (Spektrum Akademischer Verlag, Heidelberg, Germany, 1994), inter alia.

It has been found that, after overexpression of the pknD gene, the production of amino acids by corynebacteria is improved.

Overexpression can be achieved by increasing the copy number of the appropriate genes or mutating the promoter and regulatory region or the ribosome binding site located upstream from the structural gene. Expression cassettes incorporated upstream from the structural gene work in the same way. Inducible promoters additionally make it possible to increase the expression in the course of the production of amino acid by fermentation. Measures for prolonging the life of the mRNA also improve the expression. Furthermore, the enzyme activity is also enhanced by preventing the degradation of the enzyme protein. The genes or gene constructs can either be located in plasmids of variable copy number or integrated and amplified in the chromosome. Alternatively, it is also possible to achieve overexpression of the genes in question by changing the composition of the media and the culture technique.

Those skilled in the art can find relevant instructions in Martin et al. (Bio/Technology 5, 137-146 (1987)), Guerrero et al. (Gene 138, 35-41 (1994)), Tsuchiya and Morinaga (Bio/Technology 6, 428-430 (1988)), Eikmanns et al. (Gene 102, 93-98 (1991)), EP 0 472 869, U.S. Pat. No. 4,601,893, Schwarzer and Puhler (Bio/Technology 9, 84-87 (1991)), Reinscheid et al. (Applied and Environmental Microbiology 60, 126-132 (1994)), LaBarre et al. (Journal of Bacteriology 175, 1001-1007 (1993)), WO 96/15246, Malumbres et al. (Gene 134, 15-24 (1993)), JP-A-10-229891, Jensen and Hammer (Biotechnology and Bioengineering 58, 191-195 (1998)) and Makrides (Microbiological Reviews 60, 512-538 (1996)), inter alia, and in well-known textbooks on genetics and molecular biology.

For amplification, the pknD gene according to the invention has been overexpressed for example with the aid of episomal plasmids. Suitable plasmids are those which are replicated in corynebacteria. Numerous known plasmid vectors, e.g. pZ1 (Menkel et al., Applied and Environmental Microbiology (1989) 64, 549-554), pEKEx1 (Eikmanns et al., Gene 102, 93-98 (1991)) or pHS2-1 (Sonnen et al., Gene 107, 69-74 (1991)), are based on cryptic plasmids pHM1519, pBL1 or pGA1. Other plasmid vectors, e.g. those based on pCG4 (U.S. Pat. No. 4,489,160), pNG2 (Serwold-Davis et al., FEMS Microbiology Letters 66, 119-124 (1990)) or pAG1 (U.S. Pat. No. 5,158,891), can be used in the same way.

Other suitable plasmid vectors are those which make it possible to use the gene amplification process by integration into the chromosome, as described for example by Reinscheid et al. (Applied and Environmental Microbiology 60, 126-132 (1994)) for the duplication or amplification of the hom-thrB operon. In this method the complete gene is cloned into a plasmid vector which can replicate in a host (typically E. coli), but not in C. glutamicum. Examples of suitable vectors are pSUP301 (Simon et al., Bio/Technology 1, 784-791 (1983)), pK18mob or pK19mob (Schäfer et al., Gene 145, 69-73 (1994)), pGEM-T (Promega Corporation, Madison, Wis., USA), pCR2.1-TOPO (Shuman (1994), Journal of Biological Chemistry 269, 32678-84; U.S. Pat. No. 5,487,993), pCR®Blunt (Invitrogen, Groningen, The Netherlands; Bernard et al., Journal of Molecular Biology 234, 534-541 (1993)), pEM1 (Schrumpf et al., 1991, Journal of Bacteriology 173, 4510-4516) or pBGS8 (Spratt et al., 1986, Gene 41, 337-342). The plasmid vector containing the gene to be amplified is then transferred to the desired strain of C. glutamicum by conjugation or transformation. The method of conjugation is described for example in Schäfer et al. (Applied and Environmental Microbiology 60, 756-759 (1994)). Methods of transformation are described for example in Thierbach et al. (Applied Microbiology and Biotechnology 29, 356-362 (1988)), Dunican and Shivnan (Bio/Technology 7, 1067-1070 (1989)) and Tauch et al. (FEMS Microbiological Letters 123, 343-347 (1994)). After homologous recombination by means of a crossover event, the resulting strain contains at least two copies of the gene in question.

It has also been found that amino acid exchanges in the section between position 661 and position 669 of the amino acid sequence of protein kinase D, shown in SEQ ID No. 2, improve the production of amino acids, especially lysine, by corynebacteria. Preferably, L-glutamic acid in position 664 is exchanged for any other proteogenic amino acid except L-glutamic acid, and/or glycine in position 666 is exchanged for any other proteogenic amino acid except glycine.

The exchange in position 664 is preferably for L-lysine or L-arginine, especially L-lysine, and the exchange in position 666 is preferably for L-serine or L-threonine, especially L-serine.

SEQ ID No. 3 shows the base sequence of the pknD-1547 allele contained in the strain DM1547. The pknD-1547 allele codes for a protein whose amino acid sequence is shown in SEQ ID No. 4. The protein contains L-lysine in position 664 and L-serine in position 666. The DNA sequence of the pknD-1547 allele (SEQ ID No. 3) contains the base adenine in place of the base guanine contained in the pknD wild-type gene (SEQ ID No. 1) in position 2501, and the base adenine in place of the base guanine in position 2507. Mutagenesis can be carried out by conventional methods using mutagenic substances such as N-methyl-N′-nitro-N-nitrosoguanidine or ultraviolet light. Mutagenesis can also be carried out using in vitro methods such as treatment with hydroxylamine (Miller, J. H.: A Short Course in Bacterial Genetics. A Laboratory Manual and Handbook for Escherichia coli and Related Bacteria, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, 1992) or mutagenic oligonucleotides (T. A. Brown: Gentechnologie für Einsteiger (Gene Technology for Beginners), Spektrum Akademischer Verlag, Heidelberg, 1993), or the polymerase chain reaction (PCR) as-described in the manual by Newton and Graham (PCR, Spektrum Akademischer Verlag, Heidelberg, 1994).

The corresponding alleles or mutations are sequenced and introduced into the chromosome by the method of gene replacement, for example as described in Peters-Wendisch et al. (Microbiology 144, 915-927 (1998)) for the pyc gene of C. glutamicum, in Schäfer et al. (Gene 145, 69-73 (1994)) for the hom-thrB gene region of C. glutamicum or in Schäfer et al. (Journal of Bacteriology 176, 7309-7319 (1994)) for the cg1 gene region of C. glutamicum. The corresponding alleles or the associated proteins can optionally be amplified in turn.

In addition it can be advantageous for the production of L-amino acids to amplify and, in particular, overexpress not only the pknD gene but also one or more enzymes of the particular biosynthetic pathway, the glycolysis, the anaplerosis, the citric acid cycle, the pentose phosphate cycle or the amino acid export, and optionally regulatory proteins.

Thus, for the production of L-amino acids, one or more endogenous genes selected from the following group can be amplified and, in particular, overexpressed in addition to amplification of the pknD gene:

-   -   the dapA gene coding for dihydrodipicolinate synthase (EP-B-0         197 335),     -   the gap gene coding for glyceraldehyde 3-phosphate dehydrogenase         (Eikmanns (1992), Journal of Bacteriology 174, 6076-6086),     -   the tpi gene coding for triose phosphate isomerase (Eikmanns         (1992), Journal of Bacteriology 174, 6076-6086),     -   the pgk gene coding for 3-phosphoglycerate kinase (Eikmanns         (1992), Journal of Bacteriology 174, 6076-6086),     -   the zwf gene coding for glucose-6-phosphate dehydrogenase         (JP-A-09224661),     -   the pyc gene coding for pyruvate carboxylase (DE-A-198 31 609),     -   the lysC gene coding for a feedback-resistant aspartate kinase         (Accession no. P26512; EP-B-0387527; EP-A-0699759),     -   the lysE gene coding for lysine export (DE-A-195 48 222),     -   The hom gene coding for homoserine dehydrogenase (EP-A-01         31171),     -   the ilvA gene coding for threonine dehydratase (Möckel et al.,         Journal of Bacteriology (1992) 8065-8072)) or the ilvA(Fbr)         allele coding for a feedback-resistant threonine dehydratase         (Mockel et al., (1994), Molecular Microbiology 13, 833-842),     -   the ilvBN gene coding for acetohydroxy acid synthase         (EP-B-0356739),     -   the ilvD gene coding for dihydroxy acid dehydratase (Sahm and         Eggeling (1999), Applied and Environmental Microbiology 65,         1973-1979),     -   the zwa1 gene coding for the Zwa1 protein (DE 199 59 328.0,         DSM13115).

In addition to amplification of the pknD gene, it can also be advantageous for the production of L-amino acids to attenuate one or more genes selected from the following group:

-   -   the pck gene coding for phosphoenol pyruvate carboxykinase (DE         199 50 409.1, DSM13047),     -   the pgi gene coding for glucose-6-phosphate isomerase (U.S. Ser.         No. 09/396,478, DSM12969),     -   the poxB gene coding for pyruvate oxidase (DE 199 51 975.7,         DSM13114),     -   the zwa2 gene coding for the Zwa2 protein (DE 199 59 327.2,         DSM13113), and, in particular, to reduce the expression.

In this context the term “attenuation” describes the reduction or switching-off of the intracellular activity, in a microorganism, of one or more enzymes (proteins) which are coded for by the appropriate DNA, for example by using a weak promoter or using a gene or allele coding for an appropriate enzyme with a low activity, or inactivating the appropriate gene or enzyme (protein), and optionally combining these measures.

By attenuation measures, the activity or concentration of the corresponding protein is in general reduced to 0 to 75%, 0 to 50%, 0 to 25%, 0 to 10% or 0 to 5% of the a concentration of the wild-type protein or of the activity or concentration of the protein in the starting microorganism.

It can also be advantageous for the production of amino acids not only to overexpress the pknD gene but also to switch off unwanted secondary reactions (Nakayama: “Breeding of Amino Acid Producing Micro-organisms”, in: Overproduction of Microbial Products, Krumphanzl, Sikyta, Vanek (eds.), Academic Press, London, UK, 1982).

The microorganisms prepared according to the invention are also provided by the invention and can be cultivated for the production of amino acids continuously or discontinuously by the batch process, the fed batch process or the repeated fed batch process. A summary of known cultivation methods is described in the textbook by Chmiel (Bioprozesstechnik 1. Einführung in die Bioverfahrenstechnik (Bioprocess Technology 1. Introduction to Bioengineering) (Gustav Fischer Verlag, Stuttgart, 1991)) or in the textbook by Storhas (Bioreaktoren und periphere Einrichtungen (Bioreactors and Peripheral Equipment) (Vieweg Verlag, Brunswick/Wiesbaden, 1994)).

The culture medium to be used must appropriately meet the demands of the particular strains. Descriptions of culture media for various microorganisms can be found in “Manual of Methods for General Bacteriology” of the American Society for Bacteriology (Washington D.C., USA, 1981).

Carbon sources which can be used are sugars and carbohydrates, e.g. glucose, sucrose, lactose, fructose, maltose, molasses, starch and cellulose, oils and fats, e.g. soybean oil, sunflower oil, groundnut oil and coconut fat, fatty acids, e.g. palmitic acid, stearic acid and linoleic acid, alcohols, e.g. glycerol and ethanol, and organic acids, e.g. acetic acid. These substances can be used individually or as a mixture.

Nitrogen sources which can be used are organic nitrogen-containing compounds such as peptones, yeast extract, meat extract, malt extract, corn steep liquor, soybean flour and urea, or inorganic compounds such as ammonium sulfate, ammonium chloride, ammonium phosphate, ammonium carbonate and ammonium nitrate. The nitrogen sources can be used individually or as a mixture.

Phosphorus sources which can be used are phosphoric acid, potassium dihydrogenphosphate or dipotassium hydrogenphosphate or the corresponding sodium salts. The culture medium must also contain metal salts, e.g. magnesium sulfate or iron sulfate, which are necessary for growth. Finally, essential growth-promoting substances such as amino acids and vitamins can be used in addition to the substances mentioned above. Suitable precursors can also be added to the culture medium. The feed materials can be added to the culture all at once or fed in appropriately during cultivation.

The pH of the culture is controlled by the appropriate use of basic compounds such as sodium hydroxide, potassium hydroxide, ammonia or aqueous ammonia, or acidic compounds such as phosphoric acid or sulfuric acid. Foaming can be controlled using antifoams such as fatty acid polyglycol esters. The stability of plasmids can be maintained by adding suitable selectively acting substances, e.g. antibiotics, to the medium. Aerobic conditions are maintained by introducing oxygen or oxygen-containing gaseous mixtures, e.g. air, into the culture. The temperature of the culture is normally 20° C. to 45° C. and preferably 25° C. to 40° C. The culture is continued until the formation of the desired product has reached a maximum. This objective is normally achieved within 10 hours to 160 hours. Methods of determining L-amino acids are well-known in the art. They can be analyzed for example by ion exchange chromatography with subsequent ninhydrin derivation, as described by Spackman et al. (Analytical Chemistry 30 (1958) 1190), or by reversed phase HPLC, as described by Lindroth et al. (Analytical Chemistry (1979) 51, 1167-1174).

A pure culture of the Corynebacterium glutamicum strain DM1547 was deposited as DSM 13994 in the Deutsche Sammlung für Mikroorganismen und Zellkulturen (German Collection of Microorganisms and Cell Cultures (DSMZ), Brunswick, Germany) on 16 Jan. 2001 under the terms of the Budapest Treaty.

A pure culture of the Escherichia coli strain S17-1/pK18mobsacB_pknD_XL was deposited as DSM 14410 in the Deutsche Sammlung far Mikroorganismen und Zellkulturen (German Collection of Microorganisms and Cell Cultures (DSMZ, Brunswick, Germany) on 18 Jul. 2001 under the terms of the Budapest Treaty.

The fermentation process according to the invention is used for the preparation of amino acids.

The present invention also provides a method of identifying nucleic acids which code for protein kinase B or have a high degree of similarity to the sequence of the pknB gene, comprising:

contacting a sample with the polynucleotide of claim 1 under conditions suitable for the polynucleotide to hydridize to another nucleic acid which codes for protein kinase B or have a high degree of similarity to the sequence of the pknB gene.

In one embodiment, the “another nucleic acid” mentioned above may be RNA, cDNA, or DNA. In another embodiment, the method is conducted on an array, micro-array, or DNA chip.

EXAMPLES

Having generally described this invention, a further understanding can be obtained by reference to certain specific examples which are provided herein for purposes of illustration only and are not intended to be limiting unless otherwise specified.

The isolation of plasmid DNA from Escherichia coli and all the techniques of restriction, Klenow treatment and alkaline phosphatase treatment were carried out according to Sambrook et al. (Molecular Cloning. A Laboratory Manual (1989), Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., USA). Methods of transforming Escherichia coli are also described in this manual. The composition of common nutrient media, such as LB or TY medium, can also be found in the manual by Sambrook et al.

Example 1 Preparation of a Genomic Cosmid Gene Library from Corynebacterium glutamicum ATCC 13032

Chromosomal DNA from Corynebacterium glutamicum ATCC13032 was isolated as described by Tauch et al. (1995, Plasmid 33, 168-179) and partially cleaved with the restriction enzyme Sau3AI (Amersham Pharmacia, Freiburg, Germany, product description Sau3AI, code no. 27-0913-02). The DNA fragments were dephosphorylated with shrimp alkaline phosphatase (Roche Diagnostics GmbH, Mannheim, Germany, product description SAP, code no. 1758250). The DNA of cosmid vector SuperCos1 (Wahl et al. (1987), Proceedings of the National Academy of Sciences USA 84, 2160-2164), obtained from Stratagene (La Jolla, USA, product description SuperCos1 Cosmid Vector Kit, code no. 251301), was cleaved with the restriction enzyme XbaI (Amersham Pharmacia, Freiburg, Germany, product description XbaI, code no. 27-0948-02) and also dephosphorylated with shrimp alkaline phosphatase.

The cosmid DNA was then cleaved with the restriction enzyme BamHI (Amersham Pharmacia, Freiburg, Germany, product description BamHI, code no. 27-0868-04). The cosmid DNA treated in this way was mixed with the treated ATCC13032 DNA and the mixture was treated with T4 DNA ligase (Amersham Pharmacia, Freiburg, Germany, product description T4 DNA ligase, code no. 27-0870-04). The ligation mixture was then packaged into phages using Gigapack II XL Packing Extract (Stratagene, La Jolla, USA, product description Gigapack II XL Packing Extract, code no. 200217).

For infection of the E. coli strain NM554 (Raleigh et al., 1988, Nucleic Acid Research 16, 1563-1575), the cells were taken up in 10 mM MgSO₄ and mixed with an aliquot of the phage suspension. Infection and titering of the cosmid library were carried out as described by Sambrook et al. (1989, Molecular Cloning: A Laboratory Manual, Cold Spring Harbor), the cells being plated on LB agar (Lennox, 1955, Virology 1, 190) containing 100 mg/l of ampicillin. After incubation overnight at 37° C., recombinant single clones were selected.

Example 2 Isolation and Sequencing of the pknD Gene

The cosmid DNA of a single colony was isolated with the Qiaprep Spin Miniprep Kit (product no. 27106, Qiagen, Hilden, Germany) in accordance with the manufacturer's instructions and partially cleaved with the restriction enzyme Sau3AI (Amersham Pharmacia, Freiburg, Germany, product description Sau3AI, product no. 27-0913-02). The DNA fragments were dephosphorylated with shrimp alkaline phosphatase (Roche Diagnostics GmbH, Mannheim, Germany, product description SAP, product no. 1758250). After separation by gel electrophoresis, the cosmid fragments in the size range from 1500 to 2000 bp were isolated with the QiaExII Gel Extraction Kit (product no. 20021, Qiagen, Hilden, Germany).

The DNA of sequencing vector pZero-1, obtained from Invitrogen (Groningen, The Netherlands, product description Zero Background Cloning Kit, product no. K2500-01), was cleaved with the restriction enzyme BamHI (Amersham Pharmacia, Freiburg, Germany, product description BamHI, product no. 27-0868-04). Ligation of the cosmid fragments into sequencing vector pZero-1 was carried out as described by Sambrook et al. (1989, Molecular Cloning: A Laboratory Manual, Cold Spring Harbor), the DNA mixture being incubated overnight with T4 ligase (Pharmacia Biotech, Freiburg, Germany). This ligation mixture was then introduced into the E. coli strain DH5αMCR (Grant, 1990, Proceedings of the National Academy of Sciences USA 87, 4645-4649) by electroporation (Tauch et al. 1994, FEMS Microbiol. Letters 123, 343-7) and plated on LB agar (Lennox, 1955, Virology 1, 190) containing 50 mg/l of zeocin.

Plasmid preparation of the recombinant clones was carried out with Biorobot 9600 (product no. 900200, Qiagen, Hilden, Germany). Sequencing was carried out by the dideoxy chain termination method of Sanger et al. (1977, Proceedings of the National Academy of Sciences USA 74, 5463-5467) with modifications by Zimmermann et al. (1990, Nucleic Acids Research 18, 1067). The “RR dRhodamin Terminator Cycle Sequencing Kit” from PE Applied Biosystems (product no. 403044, Weiterstadt, Germany) was used. Separation by gel electrophoresis and analysis of the sequencing reaction were carried out in a “Rotiphorese NF acrylamide/bisacrylamide” gel (29:1) (product no. A124.1, Roth, Karlsruhe, Germany) with the “ABI Prism 377” sequencer from PE Applied Biosystems (Weiterstadt, Germany).

The raw sequence data obtained were then processed using the Staden programming package (1986, Nucleic Acids Research 14, 217-231), version 97-0. The individual sequences of the pZero-1 derivatives were assembled into a cohesive contig. Computer-assisted coding region analysis was performed with the XNIP program (Staden, 1986, Nucleic Acids Research 14, 217-231).

The nucleotide sequence obtained is shown in SEQ ID No. 1. Analysis of the nucleotide sequence gave an open reading frame of 2223 base pairs, which was called the pknD gene. The pknD gene codes for a protein of 740 amino acids.

Example 3 Preparation of a Replacement Vector for Replacement of the pknD Allels

Chromosomal DNA was isolated from the strain DSM13994 by the method of Eikmanns et al. (Microbiology 140:1817-1828 (1994)). On the basis of the sequence of the pknD gene known for C. glutamicum from example 2, the following oligonucleotides were chosen for the polymerase chain reaction (see also SEQ ID No. 5 and SEQ ID No. 6):

pknD_XL-A1:

-   5′ (tct aga) cgg ttg gtg gtt cgg ttc ag 3′     pknD_XL-E1: -   5′ (tct aga) agc ggc aat gcc ggt gag ta 3′

The primers shown were synthesized by MWG Biotech (Ebersberg, Germany) and the PCR reaction was carried out by the PCR method of Karreman (BioTechniques 24:736-742, 1998) with Pwo-Polymerase from Boehringer. The primers pknD_XL-A1 and pknD_XL-E1 each contain an inserted cleavage site for the restriction enzyme XbaI, these being indicated in parentheses in the representation. With the aid of the polymerase chain reaction, a 1.6 kb DNA section is amplified and isolated, this carrying the pknD gene or allele.

The amplified DNA fragment of approx. 1.6 kb length, which carries the pknD allele of the strain DSM13994, was cleaved with the restriction enzyme XbaI, identified by electrophoresis in a 0.8% agarose gel, isolated from the gel and purified by the conventional methods (QIAquick Gel Extraction Kit, Qiagen, Hilden).

The plasmid pK18mobsacB (Jäger et al., Journal of Bacteriology, 1:784-791(1992)) was also cleaved with the restriction enzyme XbaI. The plasmid pK18mobsacB and the PCR fragment were ligated. The E. coli strain S17-1 (Simon et al., 1993, Bio/Technology 1:784-791) was then electroporated with the ligation batch (Hanahan, In: DNA Cloning. A Practical Approach. Vol. I, IRL-Press, Oxford, Washington D.C., USA, 1985). Selection of plasmid-carrying cells was carried out by plating out the transformation batch on LB Agar (Sambrook et al., Molecular cloning: a laboratory manual. 2^(nd) Ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 1989), which had been supplemented with 25 mg/l kanamycin. Plasmid DNA was isolated from a transformant with the aid of the QIAprep Spin Miniprep Kit from Qiagen and checked by restriction with the restriction enzyme XbaI and subsequent agarose gel electrophoresis (0.8%). The plasmid was designated pK18mobsacB_pknD_XL and is shown in FIG. 1.

Obviously, numerous modifications and variations of the present invention are possible in light of the above teachings. It is therefore to be understood that within the scope of the appended claims, the invention may be practiced otherwise than as specifically described herein.

All of the publications cited above are incorporated herein by reference.

This application is based on German Patent Application Ser. No. 100 44 948.4, filed on Sep. 12, 2000; and German Patent Application Ser. No. 101 20 094.3, filed on Apr. 25, 2001, which are incorporated herein by reference. 

1. An isolated polynucleotide from corynebacteria comprising a polynucleotide sequence selected from the group consisting of: (a) a polynucleotide which is at least 90% identical to the polynucleotide of SEQ ID NO: 1, wherein said polynucleotide codes for a polypeptide comprising the amino acid sequence of SEQ ID NO: 2 and has protein kinase D activity, (b) a polynucleotide coding for a polypeptide comprising the amino acid sequence of SEQ ID NO: 2 and having protein kinase D activity, and (c) a polynucleotide which is complementary to the polynucleotides of(a) or (b).
 2. The pelynucleotide of claim 1, which is a recombinant DNA replicable in corynebacteria.
 3. The polynucleotide of claim 1, which is an RNA.
 4. The polynucleotide of claim 2, which comprises the nucleic acid sequence as shown in SEQ ID NO:
 1. 5. The polynucleotide of claim 2, which comprises: (i) the nucleotide sequence shown in SEQ ID NO: 1, or (ii) at least one sequence corresponding to a polynucleotide encoding a polypeptide comprising the amino acid sequence of SEQ ID NO: 2, wherein the polypeptide has protein kinase D activity, or (iii) at least one sequence which hybridizes with the sequence complementary to sequence (i) or (ii), wherein hybridization comprises washing in 0.5×SSC at a temperature of 68° C.
 6. The polynucleotide of claim 1 which codes for a polypeptide comprising the amino acid sequence shown in SEQ ID NO:
 2. 7. The polynucleotide of claim 1, which is (a).
 8. The polynucleotide of claim 1, which is (b).
 9. The polynucleotide of claim 1, which is (c).
 10. Escherichia coli strain S17-1/pK18mobsacB_pknD_XL deposited as DSM 14410 at the Deutsche Sammlung fdr Mikroorganismen und Zellkulturen (German Collection of Microorganisms and Cell Cultures), Brunswick, Germany.
 11. Corynebacteria transformed with a vector, which comprises a polynucleotide as claimed in claim
 1. 12. An isolated polynucleotide originating from corynebacteria and coding for a polypeptide having protein kinase D activity, which comprises SEQ ID No:2 and wherein amino acids between positions 661 and 669 are modified by an amino acid exchange.
 13. An isolated polynucleotide originating from corynebacteria and coding for a polypeptide having protein kinase D activity, which polypeptide comprises SEQ ID NO:2 and wherein the amino acid at position 664 in SEQ ID NO:2 is replaced with another amino acid except glutamic acid.
 14. An isolated polynucleotide originating from corynebacteria and coding for a polypeptide having protein kinase D activity, which polypeptide comprises SEQ ID NO:2 and wherein the amino acid at position 664 in SEQ ID NO:2 is replaced with L-lysine or L-arginine.
 15. An isolated polynucleotide originating from corynebacteria and coding for a polypeptide having protein kinase D activity, which polypeptide comprises SEQ NO:2 and wherein the amino acid at position 664 in SEQ ID NO:2 is replaced with L-lysine or L-arginine.
 16. An isolated polynucleotide originating from corynebacteria and coding for a polypeptide having protein kinase D activity, which polypeptide comprises SEQ ID NO:2 and wherein the amino acid at position 666 SEQ ID NO:2 is replaced with another proteogenic amino acid except glycine.
 17. An isolated polynucleotide originating from corynebacteria and coding for a polypeptide having protein kinase D activity, which polypeptide comprises SEQ ID NO:2 and wherein the amino acid at position 666 in SEQ ID NO:2 is replaced with L-serine or L-threonine.
 18. An isolated polynucleotide originating from corynebacteria and coding for a polypeptide having protein kinase D activity, which polypeptide comprises SEQ ID NO:2 and wherein the amino acid at position 666 in SEQ ID NO:2 is replaced with L-serine.
 19. An isolated polynucleotide originating from corynebacteria and coding for a polypeptide having protein kinase D activity, which polypeptide comprises SEQ ID NO:4.
 20. The isolated polynucleotide of claim 19, wherein the isolated nucleic acid or polynucleotide contains the nucleobase adenine in position 2501 and the nucleobase adenine in position 2507, shown in SEQ ID NO:3.
 21. Corynebacteria transformed with the isolated polynucleotide of claim
 13. 22. Corynebacteria transformed with the isolated polynucleotide of claim
 14. 23. Corynebacteria transformed with the isolated polynucleotide of claim
 15. 24. Corynebacteria transformed with the isolated polynucleotide of claim
 16. 25. Corynebacteria transform with the isolated polynucleotide of claim
 17. 26. Corynebacteria transformed with the isolated polynucleotide of claim
 18. 27. Corynebacteria transformed with the isolated polynucleotide of claim
 19. 28. Corynebacterium glutamicum DM 1547 deposited as DSM 13994 in the Deutsche Sammlung fur Mikroorganismen und Zellkulturen (German Collection of Microorganisms and Cell Cultures), Brunswick, Germany.
 29. An isolated polynucleotide consisting of at least 23 consecutive nucleotides selected from SEQ ID NO:1 wherein said isolated polynucleotide is a primer in a polymerase chain reaction to produce a polynucleotide encoding a polypeptide having protein kinase D activity. 